TY - JOUR
T1 - Annotating cancer variants and anti-cancer therapeutics in Reactome
AU - Milacic, Marija
AU - Haw, Robin
AU - Rothfels, Karen
AU - Wu, Guanming
AU - Croft, David
AU - Hermjakob, Henning
AU - D'Eustachio, Peter
AU - Stein, Lincoln
PY - 2012/12
Y1 - 2012/12
N2 - Reactome describes biological pathways as chemical reactions that closely mirror the actual physical interactions that occur in the cell. Recent extensions of our data model accommodate the annotation of cancer and other disease processes. First, we have extended our class of protein modifications to accommodate annotation of changes in amino acid sequence and the formation of fusion proteins to describe the proteins involved in disease processes. Second, we have added a disease attribute to reaction, pathway, and physical entity classes that uses disease ontology terms. To support the graphical representation of "cancer" pathways, we have adapted our Pathway Browser to display disease variants and events in a way that allows comparison with the wild type pathway, and shows connections between perturbations in cancer and other biological pathways. The curation of pathways associated with cancer, coupled with our efforts to create other disease-specific pathways, will interoperate with our existing pathway and network analysis tools. Using the Epidermal Growth Factor Receptor (EGFR) signaling pathway as an example, we show how Reactome annotates and presents the altered biological behavior of EGFR variants due to their altered kinase and ligand-binding properties, and the mode of action and specificity of anti-cancer therapeutics.
AB - Reactome describes biological pathways as chemical reactions that closely mirror the actual physical interactions that occur in the cell. Recent extensions of our data model accommodate the annotation of cancer and other disease processes. First, we have extended our class of protein modifications to accommodate annotation of changes in amino acid sequence and the formation of fusion proteins to describe the proteins involved in disease processes. Second, we have added a disease attribute to reaction, pathway, and physical entity classes that uses disease ontology terms. To support the graphical representation of "cancer" pathways, we have adapted our Pathway Browser to display disease variants and events in a way that allows comparison with the wild type pathway, and shows connections between perturbations in cancer and other biological pathways. The curation of pathways associated with cancer, coupled with our efforts to create other disease-specific pathways, will interoperate with our existing pathway and network analysis tools. Using the Epidermal Growth Factor Receptor (EGFR) signaling pathway as an example, we show how Reactome annotates and presents the altered biological behavior of EGFR variants due to their altered kinase and ligand-binding properties, and the mode of action and specificity of anti-cancer therapeutics.
KW - Cancer annotation
KW - EGFR signaling
KW - Network visualization
KW - Pathway database
KW - Pathway visualization
UR - http://www.scopus.com/inward/record.url?scp=84871602426&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84871602426&partnerID=8YFLogxK
U2 - 10.3390/cancers4041180
DO - 10.3390/cancers4041180
M3 - Article
C2 - 24213504
AN - SCOPUS:84871602426
SN - 2072-6694
VL - 4
SP - 1180
EP - 1211
JO - Cancers
JF - Cancers
IS - 4
ER -